Loading report..

Highlight Samples

Regex mode off

    Rename Samples

    Click here for bulk input.

    Paste two columns of a tab-delimited table here (eg. from Excel).

    First column should be the old name, second column the new name.

    Regex mode off

      Show / Hide Samples

      Regex mode off

        Export Plots

        px
        px
        X

        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.

        Choose Plots

        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        Save Settings

        You can save the toolbox settings for this report to the browser.

        Load Settings

        Choose a saved report profile from the dropdown box below:

        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.14

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-04-15, 07:38 BST based on data in: /mnt/lustre/RDS-live/downing/LSDV_PVG/121_SAMPLE_PVG/CURRENT

        ODGI

        ODGI is an optimized dynamic graph/genome implementation, for efficient analysis and manipulation of pangenome graphs structured in the variation graph model.

        Detailed ODGI stats table.

        Showing 2/2 rows and 10/14 columns.
        Sample NameLengthNodesEdgesPathsComponentsACTGN
        seqwish
        184251
        6719
        9126
        13
        1
        59785
        19693
        58115
        20645
        26013
        smooth
        177727
        7805
        10640
        13
        1
        58569
        19182
        56845
        20117
        23014

        Sum of path node distances

        For each path we iterate from node to node and count the node / nucleotide distance of nodes on the pangenome level normalized by the path length. If a node is reversed, we count the node distance twice.

        This value allows you to evaluate the sorting goodness - how linear the graph is.

           
        loading..

        For each path we iterate from node to node and count the node / nucleotide distance mean_links_length of nodes within the same path only. We then normalized by the path length.

        This value allows you to evaluate the sorting goodness - how linear the graph is.

           

        ODGI Compressed 1D visualization

        This image shows a 1D rendering of the built pangenome graph. The graph nodes are arranged from left to right, forming the pangenome sequence. Summarization of path coverage across all paths. A heatmap color-coding from https://colorbrewer2.org/#type=diverging&scheme=RdBu&n=11 is used. Dark blue means highest coverage. Dark red means lowest coverage. The path names are placed on the left. The black lines under the paths are the links, which represent the graph topology.

        ODGI 1D visualization

        This image shows a 1D rendering of the built pangenome graph. The graph nodes are arranged from left to right, forming the pangenome sequence. The colored bars represent the paths versus the pangenome sequence in a binary matrix. The path names are placed on the left. The black lines under the paths are the links, which represent the graph topology.

        ODGI 1D visualization by path position

        This shows a 1D rendering of the built pangenome graph where the paths are colored according to their nucleotide position. Light grey means a low path position, black is the highest path position.

        ODGI 1D visualization by path orientation

        This image shows a 1D rendering of the built pangenome graph where the paths are colored by orientation. Forward is black, reverse is red.

        ODGI 1D visualization by node depth

        This shows a 1D rendering of the built pangenome graph where the paths are colored according to path depth. Using the Spectra color palette with 4 levels of path depths, white indicates no depth, while grey, red, and yellow indicate depth 1, 2, and greater than or equal to 3, respectively.

        ODGI 1D visualization by uncalled bases

        This shows a 1D rendering of the built pangenome graph where the paths are colored according to the coverage of uncalled bases. The lighter the green, the higher the 'N' content of a node is.

        ODGI 2D drawing

        This image shows a 2D rendering of the built pangenome graph.

        MultiQC v1.14 - Written by Phil Ewels, available on GitHub.

        This report uses HighCharts, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.